A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interp...

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Vydáno v:	Nature communications Ročník 12; číslo 1; s. 4188 - 16
Hlavní autoři:	Lam, Margaret M. C., Wick, Ryan R., Watts, Stephen C., Cerdeira, Louise T., Wyres, Kelly L., Holt, Kathryn E.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London Nature Publishing Group UK 07.07.2021 Nature Publishing Group Nature Portfolio
Témata:	45 45/23 631/114/1314 631/326/325/2482 631/326/41/2530 692/700/478/174 Anti-Bacterial Agents - pharmacology Anti-Bacterial Agents - therapeutic use Antibiotics Antimicrobial agents Antimicrobial resistance Associated species Bacterial Proteins - genetics beta-Lactamases - genetics Carbapenemase Clinical isolates Cross Infection - diagnosis Cross Infection - drug therapy Cross Infection - epidemiology Cross Infection - microbiology Datasets as Topic Drug resistance Drug Resistance, Multiple, Bacterial - genetics Epidemiological Monitoring Epidemiology Gastrointestinal Microbiome - genetics Genome, Bacterial Genomes Genomics Genotyping Health surveillance Humanities and Social Sciences Humans Infant Infant, Newborn Interrogation Klebsiella Klebsiella Infections - diagnosis Klebsiella Infections - drug therapy Klebsiella Infections - epidemiology Klebsiella Infections - microbiology Klebsiella pneumoniae Klebsiella pneumoniae - genetics Klebsiella pneumoniae - isolation & purification Klebsiella pneumoniae - pathogenicity Metagenome - genetics Molecular Epidemiology - methods Molecular Typing - methods multidisciplinary Mutation Neonates Phylogeny Population structure Public health Science Science (multidisciplinary) Sepsis Software Virulence Virulence - genetics Virulence Factors - genetics Whole Genome Sequencing
ISSN:	2041-1723, 2041-1723
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Shrnutí:	Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella , highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes. Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 ObjectType-Undefined-3
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-021-24448-3